def __init__(self, arg=None, load=True):
""" Initialize with a single filename or a list of them,
a ConfigParser, or nothing for an empty pipeline"""
if arg is None:
arg = list()
if isinstance(arg, config.Inifile):
self.options = arg
else:
self.options = config.Inifile(arg)
#This will be set later
self.root_directory = self.options.get("runtime", "root", "cosmosis_none_signifier")
if self.root_directory=="cosmosis_none_signifier":
self.root_directory=None
self.quiet = self.options.getboolean(PIPELINE_INI_SECTION, "quiet", True)
self.debug = self.options.getboolean(PIPELINE_INI_SECTION, "debug", False)
self.timing = self.options.getboolean(PIPELINE_INI_SECTION, "timing", False)
shortcut = self.options.get(PIPELINE_INI_SECTION, "shortcut", "")
if shortcut=="": shortcut=None
# initialize modules
self.modules = []
if load and PIPELINE_INI_SECTION in self.options.sections():
module_list = self.options.get(PIPELINE_INI_SECTION,
"modules", "").split()
for module_name in module_list:
# identify module file
filename = self.find_module_file(
self.options.get(module_name, "file"))
# identify relevant functions
setup_function = self.options.get(module_name,
"setup", "setup")
exec_function = self.options.get(module_name,
"function", "execute")
cleanup_function = self.options.get(module_name,
"cleanup", "cleanup")
self.modules.append(module.Module(module_name,
filename,
setup_function,
exec_function,
cleanup_function,
self.root_directory))
self.shortcut_module=0
self.shortcut_data=None
if shortcut is not None:
try:
index = module_list.index(shortcut)
except ValueError:
raise ValueError("You tried to set a shortcut in "
"the pipeline but I do not know module %s"%shortcut)
if index == 0:
print "You set a shortcut in the pipeline but it was the first module."
print "It will make no difference."
self.shortcut_module = index
def load_priors(cls, prior_files):
priors = {}
for f in prior_files:
ini = config.Inifile(f)
for option, value in ini:
if option in priors:
raise ValueError("Duplicate prior identified")
priors[option] = cls.parse_prior(value)
return priors
def load_parameters(value_file, priors_files=None, override=None):
values_ini = config.Inifile(value_file)
if priors_files:
priors = prior.Prior.load_priors(priors_files)
else:
priors = {}
parameters = []
for (section, name), value in values_ini:
#override if available
if (override is not None) and (section, name) in override:
value = override[(section, name)]
# parse value line
start, limits = Parameter.parse_parameter(value)
# check for prior
pri = priors.get((section, name), None)
parameters.append(Parameter(section, name, start, limits, pri))
return parameters